https://launchpad.net/ubuntu/+source/blasr/5.3.3+dfsg-4build2/+build/19299061 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-031 4.4.0-178-generic #208-Ubuntu SMP Sun Apr 5 23:45:10 UTC 2020 x86_64 Buildd toolchain package versions: launchpad-buildd_189 python-lpbuildd_189 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.9 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 13 May 17:44:11 ntpdate[1923]: adjust time server 10.211.37.1 offset -0.025426 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19299061 --image-type chroot /home/buildd/filecache-default/7f6882774d93a6ce12d34cd2f4e4b83a707bcc6e Creating target for build PACKAGEBUILD-19299061 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19299061 Starting target for build PACKAGEBUILD-19299061 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19299061 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19299061 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19299061 Updating target for build PACKAGEBUILD-19299061 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [268 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [119 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main amd64 Packages [971 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [506 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe amd64 Packages [8729 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5176 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 Packages [80.9 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [36.7 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 Packages [504 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [302 kB] Fetched 16.9 MB in 7s (2438 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files cpp-9 dash debconf e2fsprogs g++-9 gcc-10-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv libacl1 libapparmor1 libapt-pkg6.0 libasan5 libatomic1 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libext2fs2 libgcc-9-dev libgcc-s1 libgomp1 libidn2-0 libitm1 liblsan0 libncurses6 libncursesw6 libperl5.30 libprocps8 libquadmath0 libseccomp2 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libtsan0 libubsan1 libudev1 linux-libc-dev logsave make ncurses-base ncurses-bin perl perl-base perl-modules-5.30 procps systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata 61 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 50.3 MB of archives. After this operation, 101 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libcrypt-dev amd64 1:4.4.15-1ubuntu1 [104 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libcrypt1 amd64 1:4.4.15-1ubuntu1 [78.2 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main amd64 base-files amd64 11ubuntu7 [60.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main amd64 libperl5.30 amd64 5.30.0-10 [3939 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main amd64 perl amd64 5.30.0-10 [224 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main amd64 perl-base amd64 5.30.0-10 [1511 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main amd64 perl-modules-5.30 all 5.30.0-10 [2738 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main amd64 debconf all 1.5.74 [121 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main amd64 dash amd64 0.5.10.2-7 [86.3 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main amd64 ncurses-bin amd64 6.2-1 [172 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main amd64 ncurses-base all 6.2-1 [18.7 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main amd64 sysvinit-utils amd64 2.96-3ubuntu1 [20.6 kB] Get:13 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libubsan1 amd64 10.1.0-1ubuntu1 [136 kB] Get:14 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libtsan0 amd64 10.1.0-1ubuntu1 [320 kB] Get:15 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libquadmath0 amd64 10.1.0-1ubuntu1 [146 kB] Get:16 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 liblsan0 amd64 10.1.0-1ubuntu1 [144 kB] Get:17 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libitm1 amd64 10.1.0-1ubuntu1 [26.3 kB] Get:18 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libgomp1 amd64 10.1.0-1ubuntu1 [101 kB] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 gcc-10-base amd64 10.1.0-1ubuntu1 [19.3 kB] Get:20 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libgcc-s1 amd64 10.1.0-1ubuntu1 [41.5 kB] Get:21 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libcc1-0 amd64 10.1.0-1ubuntu1 [41.2 kB] Get:22 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libatomic1 amd64 10.1.0-1ubuntu1 [9288 B] Get:23 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libstdc++6 amd64 10.1.0-1ubuntu1 [503 kB] Get:24 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 systemd-sysv amd64 245.5-2ubuntu2 [10.3 kB] Get:25 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 systemd-timesyncd amd64 245.5-2ubuntu2 [28.0 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main amd64 libacl1 amd64 2.2.53-8 [18.9 kB] Get:27 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libapparmor1 amd64 2.13.3-7ubuntu6 [34.3 kB] Get:28 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libcap2 amd64 1:2.34-1 [17.9 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main amd64 libcryptsetup12 amd64 2:2.3.1-1ubuntu1 [192 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main amd64 libidn2-0 amd64 2.3.0-1 [52.6 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main amd64 libseccomp2 amd64 2.4.3-1ubuntu2 [42.0 kB] Get:32 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 systemd amd64 245.5-2ubuntu2 [3797 kB] Get:33 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libsystemd0 amd64 245.5-2ubuntu2 [271 kB] Get:34 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libudev1 amd64 245.5-2ubuntu2 [78.4 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main amd64 libapt-pkg6.0 amd64 2.1.1 [839 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main amd64 gpgv amd64 2.2.20-1ubuntu1 [200 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main amd64 apt amd64 2.1.1 [1289 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main amd64 logsave amd64 1.45.6-1ubuntu1 [10.3 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main amd64 libext2fs2 amd64 1.45.6-1ubuntu1 [184 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main amd64 e2fsprogs amd64 1.45.6-1ubuntu1 [529 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main amd64 libncurses6 amd64 6.2-1 [101 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main amd64 libncursesw6 amd64 6.2-1 [132 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main amd64 libtinfo6 amd64 6.2-1 [87.1 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main amd64 libcom-err2 amd64 1.45.6-1ubuntu1 [9664 B] Get:45 http://ftpmaster.internal/ubuntu groovy/main amd64 libprocps8 amd64 2:3.3.16-4ubuntu1 [32.9 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main amd64 libss2 amd64 1.45.6-1ubuntu1 [11.3 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main amd64 procps amd64 2:3.3.16-4ubuntu1 [232 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main amd64 libsqlite3-0 amd64 3.31.1-5 [548 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main amd64 tzdata all 2020a-0ubuntu1 [293 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main amd64 libasan5 amd64 9.3.0-12ubuntu1 [395 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main amd64 g++-9 amd64 9.3.0-12ubuntu1 [8404 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main amd64 gcc-9 amd64 9.3.0-12ubuntu1 [8239 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main amd64 libstdc++-9-dev amd64 9.3.0-12ubuntu1 [1713 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main amd64 libgcc-9-dev amd64 9.3.0-12ubuntu1 [2359 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main amd64 cpp-9 amd64 9.3.0-12ubuntu1 [7489 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main amd64 gcc-9-base amd64 9.3.0-12ubuntu1 [19.5 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main amd64 gpg amd64 2.2.20-1ubuntu1 [485 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main amd64 gpgconf amd64 2.2.20-1ubuntu1 [124 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main amd64 gpg-agent amd64 2.2.20-1ubuntu1 [232 kB] Get:60 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 linux-libc-dev amd64 5.4.0-29.33 [1098 kB] Get:61 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 make amd64 4.2.1-2 [162 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 50.3 MB in 4s (12.2 MB/s) (Reading database ... 12816 files and directories currently installed.) 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Setting up libcap2:amd64 (1:2.34-1) ... Setting up tzdata (2020a-0ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed May 13 17:45:27 UTC 2020. Universal Time is now: Wed May 13 17:45:27 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up make (4.2.1-2) ... Setting up libncurses6:amd64 (6.2-1) ... Setting up libquadmath0:amd64 (10.1.0-1ubuntu1) ... Setting up libatomic1:amd64 (10.1.0-1ubuntu1) ... Setting up libss2:amd64 (1.45.6-1ubuntu1) ... Setting up libncursesw6:amd64 (6.2-1) ... Setting up logsave (1.45.6-1ubuntu1) ... Setting up libubsan1:amd64 (10.1.0-1ubuntu1) ... Setting up libcrypt-dev:amd64 (1:4.4.15-1ubuntu1) ... Setting up gpgconf (2.2.20-1ubuntu1) ... Setting up libperl5.30:amd64 (5.30.0-10) ... Setting up libcryptsetup12:amd64 (2:2.3.1-1ubuntu1) ... Setting up libcc1-0:amd64 (10.1.0-1ubuntu1) ... Setting up gpg (2.2.20-1ubuntu1) ... Setting up liblsan0:amd64 (10.1.0-1ubuntu1) ... 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Processing triggers for libc-bin (2.31-0ubuntu9) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19299061 amd64 groovy-proposed -c chroot:build-PACKAGEBUILD-19299061 --arch=amd64 --dist=groovy-proposed --nolog -A blasr_5.3.3+dfsg-4build2.dsc Initiating build PACKAGEBUILD-19299061 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-178-generic #208-Ubuntu SMP Sun Apr 5 23:45:10 UTC 2020 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-031.buildd +==============================================================================+ | blasr 5.3.3+dfsg-4build2 (amd64) 13 May 2020 17:45 | +==============================================================================+ Package: blasr Version: 5.3.3+dfsg-4build2 Source Version: 5.3.3+dfsg-4build2 Distribution: groovy-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/blasr-DemoIh/blasr-5.3.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/blasr-DemoIh' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19299061/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- blasr_5.3.3+dfsg-4build2.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-Qx1rRs/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-Qx1rRs/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Qx1rRs/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Qx1rRs/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Qx1rRs/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-Qx1rRs/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (34.8 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Qx1rRs/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (20.9 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12816 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 12), python3, meson, cmake, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev (>= 0.18.0~), libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.3+dfsg-2) Filtered Build-Depends: debhelper-compat (= 12), python3, meson, cmake, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev (>= 0.18.0~), libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.3+dfsg-2) dpkg-deb: building package 'sbuild-build-depends-blasr-dummy' in '/<>/resolver-_TcMVp/apt_archive/sbuild-build-depends-blasr-dummy.deb'. Ign:1 copy:/<>/resolver-_TcMVp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-_TcMVp/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-_TcMVp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-_TcMVp/apt_archive ./ Sources [311 B] Get:5 copy:/<>/resolver-_TcMVp/apt_archive ./ Packages [628 B] Fetched 3058 B in 0s (56.1 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install blasr build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libasn1-8-heimdal libblasr libblasr-dev libboost-dev libboost1.71-dev libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libcurl4 libdebhelper-perl libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libgtest-dev libhcrypto4-heimdal libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpbbam-dev libpbbam1.0.6 libpbcopper-dev libpbcopper1.3.0 libpbdata-dev libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libuv1 libwind0-heimdal libxml2 m4 man-db meson mime-support ninja-build pkg-config po-debconf python3 python3-minimal python3.8 python3.8-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.71-doc libboost-atomic1.71-dev libboost-chrono1.71-dev libboost-container1.71-dev libboost-context1.71-dev libboost-contract1.71-dev libboost-coroutine1.71-dev libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev libboost-filesystem1.71-dev libboost-graph1.71-dev libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev libboost-program-options1.71-dev libboost-python1.71-dev libboost-random1.71-dev libboost-regex1.71-dev libboost-serialization1.71-dev libboost-stacktrace1.71-dev libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev libboost1.71-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user libhdf5-doc liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libasn1-8-heimdal libblasr libblasr-dev libboost-dev libboost1.71-dev libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libcurl4 libdebhelper-perl libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libgtest-dev libhcrypto4-heimdal libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpbbam-dev libpbbam1.0.6 libpbcopper-dev libpbcopper1.3.0 libpbdata-dev libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libuv1 libwind0-heimdal libxml2 m4 man-db meson mime-support ninja-build pkg-config po-debconf python3 python3-minimal python3.8 python3.8-minimal sbuild-build-depends-blasr-dummy zlib1g-dev 0 upgraded, 114 newly installed, 0 to remove and 0 not upgraded. Need to get 53.2 MB of archives. After this operation, 335 MB of additional disk space will be used. 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http://ftpmaster.internal/ubuntu groovy/main amd64 libelf1 amd64 0.176-1.1build1 [44.0 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main amd64 libglib2.0-0 amd64 2.64.2-1 [1287 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main amd64 libicu66 amd64 66.1-2ubuntu2 [8520 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main amd64 libxml2 amd64 2.9.10+dfsg-5 [640 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main amd64 gettext-base amd64 0.19.8.1-10build1 [50.2 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main amd64 libkrb5support0 amd64 1.17-6ubuntu4 [30.9 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main amd64 libk5crypto3 amd64 1.17-6ubuntu4 [80.2 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main amd64 libkeyutils1 amd64 1.6.1-2ubuntu1 [10.1 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main amd64 libkrb5-3 amd64 1.17-6ubuntu4 [330 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main amd64 libgssapi-krb5-2 amd64 1.17-6ubuntu4 [121 kB] Get:31 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libbrotli1 amd64 1.0.7-6.1 [265 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main amd64 libroken18-heimdal amd64 7.7.0+dfsg-2 [41.8 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main amd64 libasn1-8-heimdal amd64 7.7.0+dfsg-2 [181 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main amd64 libheimbase1-heimdal amd64 7.7.0+dfsg-2 [29.7 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main amd64 libhcrypto4-heimdal amd64 7.7.0+dfsg-2 [88.0 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main amd64 libwind0-heimdal amd64 7.7.0+dfsg-2 [47.6 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main amd64 libhx509-5-heimdal amd64 7.7.0+dfsg-2 [107 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main amd64 libkrb5-26-heimdal amd64 7.7.0+dfsg-2 [207 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main amd64 libheimntlm0-heimdal amd64 7.7.0+dfsg-2 [15.1 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main amd64 libgssapi3-heimdal amd64 7.7.0+dfsg-2 [96.5 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [14.9 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [49.3 kB] Get:53 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libldap-common all 2.4.49+dfsg-2ubuntu2 [17.4 kB] Get:54 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libldap-2.4-2 amd64 2.4.49+dfsg-2ubuntu2 [156 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main amd64 libnghttp2-14 amd64 1.40.0-1build1 [78.7 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build1 [54.9 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main amd64 libssh-4 amd64 0.9.3-2ubuntu2 [170 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main amd64 libcurl4 amd64 7.68.0-1ubuntu2 [233 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main amd64 libjsoncpp1 amd64 1.7.4-3.1ubuntu2 [75.6 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main amd64 librhash0 amd64 1.3.9-1 [113 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main amd64 cmake amd64 3.16.3-3ubuntu1 [3666 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main amd64 libtool all 2.4.6-14 [161 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main amd64 dh-autoreconf all 19 [16.1 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main amd64 libdebhelper-perl all 13ubuntu1 [62.5 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:67 http://ftpmaster.internal/ubuntu groovy/main amd64 libfile-stripnondeterminism-perl all 1.8.0-1 [16.2 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main amd64 dh-strip-nondeterminism all 1.8.0-1 [5228 B] Get:69 http://ftpmaster.internal/ubuntu groovy/main amd64 dwz amd64 0.13-5 [151 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main amd64 libcroco3 amd64 0.6.13-1 [82.5 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main amd64 gettext amd64 0.19.8.1-10build1 [895 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main amd64 po-debconf all 1.0.21 [233 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main amd64 debhelper all 13ubuntu1 [877 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/universe amd64 googletest all 1.10.0-3 [623 kB] Get:76 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 hdf5-helpers amd64 1.10.6+repack-2 [13.7 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/universe amd64 libaec0 amd64 1.0.4-1 [19.1 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/universe amd64 libsz2 amd64 1.0.4-1 [5188 B] Get:79 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 libhdf5-103-1 amd64 1.10.6+repack-2 [1155 kB] Get:80 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 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groovy/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu1 [156 kB] Get:99 http://ftpmaster.internal/ubuntu groovy/main amd64 libjpeg-turbo8 amd64 2.0.3-0ubuntu1 [118 kB] Get:100 http://ftpmaster.internal/ubuntu groovy/main amd64 libjpeg-turbo8-dev amd64 2.0.3-0ubuntu1 [238 kB] Get:101 http://ftpmaster.internal/ubuntu groovy/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:102 http://ftpmaster.internal/ubuntu groovy/main amd64 libjpeg8-dev amd64 8c-2ubuntu8 [1552 B] Get:103 http://ftpmaster.internal/ubuntu groovy/main amd64 libjpeg-dev amd64 8c-2ubuntu8 [1546 B] Get:104 http://ftpmaster.internal/ubuntu groovy/universe amd64 libaec-dev amd64 1.0.4-1 [16.9 kB] Get:105 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 libhdf5-dev amd64 1.10.6+repack-2 [2427 kB] Get:106 http://ftpmaster.internal/ubuntu groovy/main amd64 liblzma-dev amd64 5.2.4-1 [145 kB] Get:107 http://ftpmaster.internal/ubuntu groovy/universe amd64 libhts-dev amd64 1.10.2-3 [92.0 kB] Get:108 http://ftpmaster.internal/ubuntu groovy/main amd64 libssl-dev amd64 1.1.1f-1ubuntu2 [1582 kB] Get:109 http://ftpmaster.internal/ubuntu groovy/universe amd64 libpbbam-dev amd64 1.0.6+dfsg-2build1 [75.4 kB] Get:110 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 libpbihdf-dev all 5.3.3+dfsg-4build2 [46.9 kB] Get:111 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 libpbseq-dev amd64 5.3.3+dfsg-4build2 [3232 B] Get:112 http://ftpmaster.internal/ubuntu groovy/universe amd64 ninja-build amd64 1.10.0-1build1 [107 kB] Get:113 http://ftpmaster.internal/ubuntu groovy/universe amd64 meson all 0.54.1-2ubuntu1 [396 kB] Get:114 http://ftpmaster.internal/ubuntu groovy/main amd64 pkg-config amd64 0.29.2-1ubuntu1 [46.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 53.2 MB in 3s (15.7 MB/s) Selecting previously unselected package libpython3.8-minimal:amd64. (Reading database ... 12816 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.2-1ubuntu1.1_amd64.deb ... Unpacking libpython3.8-minimal:amd64 (3.8.2-1ubuntu1.1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.2.9-1build1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.9-1build1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.2-1ubuntu1.1_amd64.deb ... Unpacking python3.8-minimal (3.8.2-1ubuntu1.1) ... Setting up libpython3.8-minimal:amd64 (3.8.2-1ubuntu1.1) ... Setting up libexpat1:amd64 (2.2.9-1build1) ... Setting up python3.8-minimal (3.8.2-1ubuntu1.1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13107 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.2-0ubuntu2_amd64.deb ... Unpacking python3-minimal (3.8.2-0ubuntu2) ... 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Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-6ubuntu4) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up libpbcopper-dev:amd64 (1.6.0+dfsg-1) ... Setting up libssh-4:amd64 (0.9.3-2ubuntu2) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.0-1) ... Setting up libhdf5-103-1:amd64 (1.10.6+repack-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.6+repack-2) ... Setting up libjpeg8-dev:amd64 (8c-2ubuntu8) ... Setting up libhdf5-hl-100:amd64 (1.10.6+repack-2) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10build1) ... Setting up libhx509-5-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu8) ... Setting up libpbdata-dev (5.3.3+dfsg-4build2) ... Setting up meson (0.54.1-2ubuntu1) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.6+repack-2) ... Setting up libhdf5-fortran-102:amd64 (1.10.6+repack-2) ... Setting up libhdf5-hl-fortran-100:amd64 (1.10.6+repack-2) ... Setting up libkrb5-26-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21) ... Setting up libheimntlm0-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libhdf5-dev (1.10.6+repack-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libpbihdf-dev (5.3.3+dfsg-4build2) ... Setting up libldap-2.4-2:amd64 (2.4.49+dfsg-2ubuntu2) ... Setting up libcurl3-gnutls:amd64 (7.68.0-1ubuntu2) ... Setting up libcurl4:amd64 (7.68.0-1ubuntu2) ... Setting up libhts3:amd64 (1.10.2-3) ... Setting up libhts-dev:amd64 (1.10.2-3) ... Setting up libpbbam1.0.6:amd64 (1.0.6+dfsg-2build1) ... Setting up cmake (3.16.3-3ubuntu1) ... Setting up libpbbam-dev (1.0.6+dfsg-2build1) ... Setting up libblasr (5.3.3+dfsg-4build2) ... Setting up libblasr-dev (5.3.3+dfsg-4build2) ... Setting up libpbseq-dev (5.3.3+dfsg-4build2) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13ubuntu1) ... Setting up sbuild-build-depends-blasr-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu9) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-178-generic amd64 (x86_64) Toolchain package versions: binutils_2.34-6ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-12ubuntu1 gcc-9_9.3.0-12ubuntu1 libc6-dev_2.31-0ubuntu9 libstdc++-9-dev_9.3.0-12ubuntu1 libstdc++6_10.1.0-1ubuntu1 linux-libc-dev_5.4.0-29.33 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.1 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu7 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-6ubuntu1 binutils-common_2.34-6ubuntu1 binutils-x86-64-linux-gnu_2.34-6ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.34-0.1ubuntu9 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110ubuntu1 cmake_3.16.3-3ubuntu1 cmake-data_3.16.3-3ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-12ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 fdisk_2.34-0.1ubuntu9 file_1:5.38-4 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-12ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10.1.0-1ubuntu1 gcc-9_9.3.0-12ubuntu1 gcc-9-base_9.3.0-12ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 googletest_1.10.0-3 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-0ubuntu4 hdf5-helpers_1.10.6+repack-2 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapparmor1_2.13.3-7ubuntu6 libapt-pkg6.0_2.1.1 libarchive-zip-perl_1.68-1 libarchive13_3.4.2-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-12ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7ubuntu2 libatomic1_10.1.0-1ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.34-6ubuntu1 libblasr_5.3.3+dfsg-4build2 libblasr-dev_5.3.3+dfsg-4build2 libblkid1_2.34-0.1ubuntu9 libboost-dev_1.71.0.0ubuntu2 libboost1.71-dev_1.71.0-6ubuntu6 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.31-0ubuntu9 libc-dev-bin_2.31-0ubuntu9 libc6_2.31-0ubuntu9 libc6-dev_2.31-0ubuntu9 libcap-ng0_0.7.9-2.1build1 libcap2_1:2.34-1 libcc1-0_10.1.0-1ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.15-1ubuntu1 libcrypt1_1:4.4.15-1ubuntu1 libcryptsetup12_2:2.3.1-1ubuntu1 libctf-nobfd0_2.34-6ubuntu1 libctf0_2.34-6ubuntu1 libcurl3-gnutls_7.68.0-1ubuntu2 libcurl4_7.68.0-1ubuntu2 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.251ubuntu1 libdebhelper-perl_13ubuntu1 libdeflate0_1.5-3 libdevmapper1.02.1_2:1.02.167-1ubuntu1 libdpkg-perl_1.19.7ubuntu3 libelf1_0.176-1.1build1 libexpat1_2.2.9-1build1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.24-1 libfdisk1_2.34-0.1ubuntu9 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libgcc-9-dev_9.3.0-12ubuntu1 libgcc-s1_10.1.0-1ubuntu1 libgcrypt20_1.8.5-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_10.1.0-1ubuntu1 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2ubuntu1 libgomp1_10.1.0-1ubuntu1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-6ubuntu4 libgssapi3-heimdal_7.7.0+dfsg-2 libgtest-dev_1.10.0-3 libhcrypto4-heimdal_7.7.0+dfsg-2 libhdf5-103-1_1.10.6+repack-2 libhdf5-cpp-103-1_1.10.6+repack-2 libhdf5-dev_1.10.6+repack-2 libhdf5-fortran-102_1.10.6+repack-2 libhdf5-hl-100_1.10.6+repack-2 libhdf5-hl-cpp-100_1.10.6+repack-2 libhdf5-hl-fortran-100_1.10.6+repack-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libhx509-5-heimdal_7.7.0+dfsg-2 libicu66_66.1-2ubuntu2 libidn2-0_2.3.0-1 libip4tc2_1.8.4-3ubuntu2 libisl22_0.22.1-1 libitm1_10.1.0-1ubuntu1 libjpeg-dev_8c-2ubuntu8 libjpeg-turbo8_2.0.3-0ubuntu1 libjpeg-turbo8-dev_2.0.3-0ubuntu1 libjpeg8_8c-2ubuntu8 libjpeg8-dev_8c-2ubuntu8 libjson-c4_0.13.1+dfsg-7 libjsoncpp1_1.7.4-3.1ubuntu2 libk5crypto3_1.17-6ubuntu4 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27-1ubuntu2 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-6ubuntu4 libkrb5support0_1.17-6ubuntu4 libldap-2.4-2_2.4.49+dfsg-2ubuntu2 libldap-common_2.4.49+dfsg-2ubuntu2 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_10.1.0-1ubuntu1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1ubuntu9 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1build1 libnpth0_1.6-1 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpbbam-dev_1.0.6+dfsg-2build1 libpbbam1.0.6_1.0.6+dfsg-2build1 libpbcopper-dev_1.6.0+dfsg-1 libpbcopper1.3.0_1.6.0+dfsg-1 libpbdata-dev_5.3.3+dfsg-4build2 libpbihdf-dev_5.3.3+dfsg-4build2 libpbseq-dev_5.3.3+dfsg-4build2 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12build1 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libprocps8_2:3.3.16-4ubuntu1 libpsl5_0.21.0-1ubuntu1 libpython3-stdlib_3.8.2-0ubuntu2 libpython3.8-minimal_3.8.2-1ubuntu1.1 libpython3.8-stdlib_3.8.2-1ubuntu1.1 libquadmath0_10.1.0-1ubuntu1 libreadline8_8.0-4 librhash0_1.3.9-1 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1ubuntu2 libselinux1_3.0-1build2 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu9 libsqlite3-0_3.31.1-5 libss2_1.45.6-1ubuntu1 libssh-4_0.9.3-2ubuntu2 libssl-dev_1.1.1f-1ubuntu2 libssl1.1_1.1.1f-1ubuntu2 libstdc++-9-dev_9.3.0-12ubuntu1 libstdc++6_10.1.0-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_245.5-2ubuntu2 libsz2_1.0.4-1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10.1.0-1ubuntu1 libubsan1_10.1.0-1ubuntu1 libuchardet0_0.0.6-3build1 libudev1_245.5-2ubuntu2 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu9 libuv1_1.35.0-2ubuntu1 libwind0-heimdal_7.7.0+dfsg-2 libxml2_2.9.10+dfsg-5 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.0-29.33 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu5 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 meson_0.54.1-2ubuntu1 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu9 ncurses-base_6.2-1 ncurses-bin_6.2-1 ninja-build_1.10.0-1build1 openssl_1.1.1f-1ubuntu2 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu5 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 pinentry-curses_1.1.0-3build1 pkg-config_0.29.2-1ubuntu1 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-4ubuntu1 python3_3.8.2-0ubuntu2 python3-minimal_3.8.2-0ubuntu2 python3.8_3.8.2-1ubuntu1.1 python3.8-minimal_3.8.2-1ubuntu1.1 readline-common_8.0-4 sbuild-build-depends-blasr-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 systemd_245.5-2ubuntu2 systemd-sysv_245.5-2ubuntu2 systemd-timesyncd_245.5-2ubuntu2 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.02.11.2 util-linux_2.34-0.1ubuntu9 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed May 13 17:45:40 2020 UTC gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./blasr_5.3.3+dfsg-4build2.dsc dpkg-source: info: extracting blasr in blasr-5.3.3+dfsg dpkg-source: info: unpacking blasr_5.3.3+dfsg.orig.tar.xz dpkg-source: info: unpacking blasr_5.3.3+dfsg-4build2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_pblibs.patch dpkg-source: info: applying 2to3.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19299061 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19299061 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19299061 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package blasr dpkg-buildpackage: info: source version 5.3.3+dfsg-4build2 dpkg-buildpackage: info: source distribution groovy dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --buildsystem=meson dh_auto_clean -O--buildsystem=meson dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules build dh build --buildsystem=meson dh_update_autotools_config -O--buildsystem=meson dh_autoreconf -O--buildsystem=meson debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/blasr-5.3.3+dfsg' LDFLAGS="-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5" CPPFLAGS="-isystem /usr/include/hdf5/serial" meson -Dtests=false -Dprefix=/usr build . The Meson build system Version: 0.54.1 Source dir: /<>/blasr-5.3.3+dfsg Build dir: /<>/blasr-5.3.3+dfsg/build Build type: native build Project name: blasr Project version: 5.3.3 Using 'CXXFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14' Using 'LDFLAGS' from environment with value: '-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5' Using 'CPPFLAGS' from environment with value: '-isystem /usr/include/hdf5/serial' Using 'CXXFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14' Using 'LDFLAGS' from environment with value: '-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5' Using 'CPPFLAGS' from environment with value: '-isystem /usr/include/hdf5/serial' C++ compiler for the host machine: c++ (gcc 9.3.0 "c++ (Ubuntu 9.3.0-12ubuntu1) 9.3.0") C++ linker for the host machine: c++ ld.bfd 2.34 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor -Wdelete-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-non-virtual-dtor -Wnon-virtual-dtor: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable -Wunused-but-set-variable: YES Compiler for C++ supports arguments -Wno-unused-variable -Wunused-variable: YES Run-time dependency threads found: YES Run-time dependency Boost found: YES 1.71.0 (/usr/include) Library pbbam found: YES Found pkg-config: /usr/bin/pkg-config (0.29.2) Run-time dependency libblasr found: YES 5.3.3 Run-time dependency zlib found: YES 1.2.11 Library pbcopper found: YES Configuring BlasrVersion.h using configuration Build targets in project: 5 Found ninja-1.10.0 at /usr/bin/ninja make[1]: Leaving directory '/<>/blasr-5.3.3+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/<>/blasr-5.3.3+dfsg' ln -s build obj-x86_64-linux-gnu dh_auto_build cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/25] /usr/bin/meson --internal vcstagger ../BlasrGitHash.h.in BlasrGitHash.h '' /<>/blasr-5.3.3+dfsg @BLASR_GIT_SHA1@ '(.*)' /<>/blasr-5.3.3+dfsg/git describe --always '--dirty=*' [2/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/extrautils_SAModify.cpp.o' -MF 'blasr_impl@sta/extrautils_SAModify.cpp.o.d' -o 'blasr_impl@sta/extrautils_SAModify.cpp.o' -c ../extrautils/SAModify.cpp [3/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' -MF 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o.d' -o 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' -c ../extrautils/SuffixArrayToBWT.cpp In file included from ../extrautils/SuffixArrayToBWT.cpp:4: /usr/include/pbseq/alignment/bwt/BWT.hpp: In member function ‘void Bwt::InitializeDNACharacterCount() [with T_BWT_Sequence = PackedDNASequence; T_DNASequence = FASTASequence]’: /usr/include/pbseq/alignment/bwt/BWT.hpp:192:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 192 | charCount[0]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:193:17: note: here 193 | case 0: //A | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:194:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 194 | charCount[1]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:195:17: note: here 195 | case 1: //C | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:196:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 196 | charCount[2]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:197:17: note: here 197 | case 2: //G | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:198:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 198 | charCount[3]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:199:17: note: here 199 | case 3: //T | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:200:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 200 | charCount[4]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here 201 | case 4: //N | ^~~~ [4/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' -MF 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o.d' -o 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' -c ../extrautils/BwtToSuffixArray.cpp [5/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' -MF 'blasr_impl@sta/extrautils_SWMatcher.cpp.o.d' -o 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' -c ../extrautils/SWMatcher.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/9/bits/alloc_traits.h:484:4: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/9/bits/stl_vector.h:1189:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h:33, from /usr/include/c++/9/bits/allocator.h:46, from /usr/include/c++/9/string:41, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from ../extrautils/SWMatcher.cpp:2: /usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [6/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' -MF 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o.d' -o 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' -c ../extrautils/ExciseRepeats.cpp [7/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/extrautils_SALS.cpp.o' -MF 'blasr_impl@sta/extrautils_SALS.cpp.o.d' -o 'blasr_impl@sta/extrautils_SALS.cpp.o' -c ../extrautils/SALS.cpp [8/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' -MF 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o.d' -o 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' -c ../extrautils/SimpleShredder.cpp [9/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/extrautils_Evolve.cpp.o' -MF 'blasr_impl@sta/extrautils_Evolve.cpp.o.d' -o 'blasr_impl@sta/extrautils_Evolve.cpp.o' -c ../extrautils/Evolve.cpp [10/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' -MF 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o.d' -o 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' -c ../extrautils/BuildSequenceDB.cpp [11/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' -MF 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o.d' -o 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' -c ../extrautils/PrintTupleCountTable.cpp [12/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/utils_SamToM4.cpp.o' -MF 'blasr_impl@sta/utils_SamToM4.cpp.o.d' -o 'blasr_impl@sta/utils_SamToM4.cpp.o' -c ../utils/SamToM4.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/9/bits/alloc_traits.h:484:4: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/9/bits/stl_vector.h:1189:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h:33, from /usr/include/c++/9/bits/allocator.h:46, from /usr/include/c++/9/string:41, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from ../utils/SamToM4.cpp:19: /usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [13/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' -MF 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o.d' -o 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' -c ../extrautils/StoreQualityByContextFromCmpH5.cpp In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:2: /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^~~~~ /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’ /usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/9/bits/alloc_traits.h:484:4: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/9/bits/stl_vector.h:1189:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h:33, from /usr/include/c++/9/bits/allocator.h:46, from /usr/include/c++/9/vector:64, from /usr/include/pbseq/alignment/datastructures/alignment/CmpFile.hpp:4, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:1: /usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [14/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/utils_SDPMatcher.cpp.o' -MF 'blasr_impl@sta/utils_SDPMatcher.cpp.o.d' -o 'blasr_impl@sta/utils_SDPMatcher.cpp.o' -c ../utils/SDPMatcher.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/9/bits/alloc_traits.h:484:4: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/9/bits/stl_vector.h:1189:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h:33, from /usr/include/c++/9/bits/allocator.h:46, from /usr/include/c++/9/string:41, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from ../utils/SDPMatcher.cpp:3: /usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [15/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' -MF 'blasr_impl@sta/utils_SamToCmpH5.cpp.o.d' -o 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' -c ../utils/SamToCmpH5.cpp In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFAlnGroupGroup.hpp:6, from /usr/include/pbseq/hdf/HDFCmpFile.hpp:12, from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:7, from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^~~~~ /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’ /usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/9/bits/alloc_traits.h:484:4: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/9/bits/stl_vector.h:1189:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h:33, from /usr/include/c++/9/bits/allocator.h:46, from /usr/include/c++/9/string:41, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from ../utils/SamToCmpH5.cpp:1: /usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:79, from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp: In instantiation of ‘unsigned int AlignmentSetToCmpH5Adapter::StoreRefGroup(std::string, T_CmpFile&) [with T_CmpFile = HDFCmpFile >; std::string = std::__cxx11::basic_string]’: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:136:31: required from ‘void AlignmentSetToCmpH5Adapter::StoreAlignmentCandidate(AlignmentCandidate<>&, int, T_CmpFile&, int, bool) [with T_CmpFile = HDFCmpFile >]’ /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:246:9: required from ‘void AlignmentSetToCmpH5Adapter::StoreAlignmentCandidateList(std::vector >&, T_CmpFile&, int, bool) [with T_CmpFile = HDFCmpFile >]’ ../utils/SamToCmpH5.cpp:199:98: required from here /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:64:45: warning: implicitly-declared ‘RefGroupNameId& RefGroupNameId::operator=(const RefGroupNameId&)’ is deprecated [-Wdeprecated-copy] 64 | refNameToRefGroupNameandId[refName] = RefGroupNameId(refGroupName, refGroupId); In file included from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:28:5: note: because ‘RefGroupNameId’ has user-provided ‘RefGroupNameId::RefGroupNameId(const RefGroupNameId&)’ 28 | RefGroupNameId(const RefGroupNameId &rhs) | ^~~~~~~~~~~~~~ [16/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/utils_PulseToFasta.cpp.o' -MF 'blasr_impl@sta/utils_PulseToFasta.cpp.o.d' -o 'blasr_impl@sta/utils_PulseToFasta.cpp.o' -c ../utils/PulseToFasta.cpp In file included from ../utils/PulseToFasta.cpp:8: /usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: /usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 549 | } catch (DataSetIException e) { | ^ In file included from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../utils/PulseToFasta.cpp:5: /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’: ../utils/PulseToFasta.cpp:157:41: required from here /usr/include/pbseq/hdf/HDFBasReader.hpp:760:11: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 760 | } catch (H5::DataSetIException e) { | ^~~~~ /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = FASTASequence]’: /usr/include/pbseq/hdf/HDFBasReader.hpp:726:25: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’ ../utils/PulseToFasta.cpp:157:41: required from here /usr/include/pbseq/hdf/HDFBasReader.hpp:647:11: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 647 | } catch (H5::DataSetIException e) { | ^~~~~ [17/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/utils_SamFilter.cpp.o' -MF 'blasr_impl@sta/utils_SamFilter.cpp.o.d' -o 'blasr_impl@sta/utils_SamFilter.cpp.o' -c ../utils/SamFilter.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/9/bits/alloc_traits.h:484:4: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/9/bits/stl_vector.h:1189:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h:33, from /usr/include/c++/9/bits/allocator.h:46, from /usr/include/c++/9/string:41, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from ../utils/SamFilter.cpp:29: /usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [18/25] c++ -Isawriter@exe -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ 'sawriter@exe/utils_SAWriter.cpp.o' -MF 'sawriter@exe/utils_SAWriter.cpp.o.d' -o 'sawriter@exe/utils_SAWriter.cpp.o' -c ../utils/SAWriter.cpp [19/25] c++ -ItoAfg@exe -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ 'toAfg@exe/utils_ToAfg.cpp.o' -MF 'toAfg@exe/utils_ToAfg.cpp.o.d' -o 'toAfg@exe/utils_ToAfg.cpp.o' -c ../utils/ToAfg.cpp In file included from ../utils/ToAfg.cpp:9: /usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: /usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 549 | } catch (DataSetIException e) { | ^ [20/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ 'blasr_impl@sta/utils_LoadPulses.cpp.o' -MF 'blasr_impl@sta/utils_LoadPulses.cpp.o.d' -o 'blasr_impl@sta/utils_LoadPulses.cpp.o' -c ../utils/LoadPulses.cpp In file included from ../utils/LoadPulses.cpp:19: /usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: /usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 549 | } catch (DataSetIException e) { | ^ In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = std::__cxx11::basic_string; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from ‘void HDFArray::Write(const T*, int) [with T = std::__cxx11::basic_string]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^~~~~ /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned int; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from ‘void HDFArray::Write(const T*, int) [with T = unsigned int]’ /usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = float; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’ /usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’: /usr/include/pbseq/hdf/HDFBasReader.hpp:135:28: required from ‘DNALength T_HDFBasReader::GetReadAt(UInt, SMRTSequence&) [with T_Sequence = FASTASequence; DNALength = unsigned int; UInt = unsigned int]’ ../utils/LoadPulses.cpp:680:59: required from here /usr/include/pbseq/hdf/HDFBasReader.hpp:760:11: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 760 | } catch (H5::DataSetIException e) { | ^~~~~ In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = unsigned char; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = unsigned char; UInt = unsigned int]’ ../utils/LoadPulses.cpp:1525:62: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 146 | } catch (H5::DataSetIException e) { | ^~~~~ /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = char; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = char; UInt = unsigned int]’ ../utils/LoadPulses.cpp:1537:64: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long unsigned int]’: /usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from ‘void HDFArray::WriteToPos(const T*, int, UInt) [with T = short unsigned int; UInt = unsigned int]’ ../utils/LoadPulses.cpp:1547:76: required from here /usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/9/bits/alloc_traits.h:484:4: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/9/bits/stl_vector.h:1189:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h:33, from /usr/include/c++/9/bits/allocator.h:46, from /usr/include/c++/9/bits/stl_tree.h:64, from /usr/include/c++/9/map:60, from ../utils/LoadPulses.cpp:6: /usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = FASTASequence]’: /usr/include/pbseq/hdf/HDFBasReader.hpp:726:25: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’ /usr/include/pbseq/hdf/HDFBasReader.hpp:135:28: required from ‘DNALength T_HDFBasReader::GetReadAt(UInt, SMRTSequence&) [with T_Sequence = FASTASequence; DNALength = unsigned int; UInt = unsigned int]’ ../utils/LoadPulses.cpp:680:59: required from here /usr/include/pbseq/hdf/HDFBasReader.hpp:647:11: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 647 | } catch (H5::DataSetIException e) { | ^~~~~ [21/25] rm -f libblasr_impl.a && gcc-ar csrD libblasr_impl.a 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' 'blasr_impl@sta/extrautils_SAModify.cpp.o' 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' 'blasr_impl@sta/extrautils_SALS.cpp.o' 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' 'blasr_impl@sta/extrautils_Evolve.cpp.o' 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' 'blasr_impl@sta/utils_SamToM4.cpp.o' 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' 'blasr_impl@sta/utils_SDPMatcher.cpp.o' 'blasr_impl@sta/utils_LoadPulses.cpp.o' 'blasr_impl@sta/utils_PulseToFasta.cpp.o' 'blasr_impl@sta/utils_SamFilter.cpp.o' [22/25] c++ -o sawriter 'sawriter@exe/utils_SAWriter.cpp.o' -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a -pthread -lpbbam /usr/lib/x86_64-linux-gnu/libblasr.so /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/x86_64-linux-gnu/libz.so -lpbbam -lpbcopper -Wl,--end-group '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<>/blasr-5.3.3+dfsg/build/ /usr/bin/ld: warning: libpbcopper.so.1.3.0, needed by /usr/lib/x86_64-linux-gnu/libpbbam.so, not found (try using -rpath or -rpath-link) [23/25] c++ -o toAfg 'toAfg@exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a -pthread -lpbbam /usr/lib/x86_64-linux-gnu/libblasr.so /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/x86_64-linux-gnu/libz.so -lpbbam -lpbcopper -Wl,--end-group '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<>/blasr-5.3.3+dfsg/build/ /usr/bin/ld: warning: libpbcopper.so.1.3.0, needed by /usr/lib/x86_64-linux-gnu/libpbbam.so, not found (try using -rpath or -rpath-link) [24/25] c++ -Iblasr@exe -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -DBOOST_ALL_DYN_LINK -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ 'blasr@exe/Blasr.cpp.o' -MF 'blasr@exe/Blasr.cpp.o.d' -o 'blasr@exe/Blasr.cpp.o' -c ../Blasr.cpp In file included from ../iblasr/BlasrMiscs.hpp:56, from ../iblasr/BlasrAlign.hpp:5, from ../Blasr.cpp:3: ../iblasr/BlasrMiscsImpl.hpp: In function ‘void MakeSubreadIntervals(std::vector&, std::vector&)’: ../iblasr/BlasrMiscsImpl.hpp:136:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 136 | for (auto subread : subreads) { | ^~~~~~~~ In file included from /usr/include/pbseq/pbdata/CCSSequence.hpp:5, from /usr/include/pbseq/alignment/files/CCSIterator.hpp:4, from ../iblasr/BlasrHeaders.h:57, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from ../iblasr/BlasrUtils.hpp:138, from ../iblasr/BlasrAlignImpl.hpp:4, from ../iblasr/BlasrAlign.hpp:67, from ../Blasr.cpp:3: ../iblasr/BlasrUtilsImpl.hpp: In function ‘void PrintAlignment(T_AlignmentCandidate&, SMRTSequence&, MappingParameters&, AlignmentContext&, std::ostream&, SMRTSequence&, PacBio::BAM::IRecordWriter*)’: ../iblasr/BlasrUtilsImpl.hpp:976:36: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=] 976 | } catch (std::ostream::failure f) { | ^ In file included from ../iblasr/MappingIPC.h:5, from ../iblasr/BlasrHeaders.h:99, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: ../iblasr/MappingParameters.h: In copy constructor ‘MappingParameters::MappingParameters(const MappingParameters&)’: ../iblasr/MappingParameters.h:19:7: warning: implicitly-declared ‘constexpr AnchorParameters::AnchorParameters(const AnchorParameters&)’ is deprecated [-Wdeprecated-copy] 19 | class MappingParameters | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/anchoring/BWTSearch.hpp:7, from ../iblasr/BlasrHeaders.h:42, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/datastructures/anchoring/AnchorParameters.hpp:33:23: note: because ‘AnchorParameters’ has user-provided ‘AnchorParameters& AnchorParameters::operator=(const AnchorParameters&)’ 33 | AnchorParameters &operator=(const AnchorParameters &rhs); | ^~~~~~~~ ../Blasr.cpp: In function ‘void MapReadsNonCCS(MappingData >, FASTASequence, DNATuple>*, MappingBuffers&, SMRTSequence&, SMRTSequence&, std::vector&, MappingParameters&, const int&, ReadAlignments&, std::ofstream&)’: ../Blasr.cpp:382:49: note: synthesized method ‘MappingParameters::MappingParameters(const MappingParameters&)’ first required here 382 | MappingParameters sensitiveParams = params; | ^~~~~~ ../Blasr.cpp: In function ‘int main(int, char**)’: ../Blasr.cpp:1407:51: warning: cast between incompatible function types from ‘void (*)(MappingData >, FASTASequence, DNATuple>*)’ to ‘void* (*)(void*)’ [-Wcast-function-type] 1407 | (void *(*)(void *))MapReads, &mapdb[procIndex]); | ^~~~~~~~ ../Blasr.cpp:1462:37: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 1462 | } catch (std::exception e) { | ^ In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29, from ../iblasr/BlasrHeaders.h:60, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In instantiation of ‘void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:167:25: required from ‘void BAMOutput::PrintAlignment(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::IRecordWriter&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:953:65: required from here /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:45: warning: the compiler can assume that the address of ‘read’ will never be NULL [-Waddress] 27 | if (dynamic_cast(&read) == NULL) { | ^ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/9/bits/alloc_traits.h:484:4: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/include/c++/9/bits/stl_vector.h:1189:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h:33, from /usr/include/c++/9/bits/allocator.h:46, from /usr/include/c++/9/string:41, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from ../iblasr/BlasrHeaders.h:10, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/c++/9/ext/new_allocator.h:147:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29, from ../iblasr/BlasrHeaders.h:60, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In function ‘void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence]’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:5: warning: nonnull argument ‘read’ compared to NULL [-Wnonnull-compare] 27 | if (dynamic_cast(&read) == NULL) { | ^~ [25/25] c++ -o blasr 'blasr@exe/Blasr.cpp.o' -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a -pthread -lpbbam /usr/lib/x86_64-linux-gnu/libblasr.so /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/x86_64-linux-gnu/libz.so -lpbbam -lpbcopper -Wl,--end-group '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<>/blasr-5.3.3+dfsg/build/ /usr/bin/ld: warning: libpbcopper.so.1.3.0, needed by /usr/lib/x86_64-linux-gnu/libpbbam.so, not found (try using -rpath or -rpath-link) make[1]: Leaving directory '/<>/blasr-5.3.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/blasr-5.3.3+dfsg' echo Tests require data not available in the source distribution Tests require data not available in the source distribution make[1]: Leaving directory '/<>/blasr-5.3.3+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --buildsystem=meson dh_testroot -O--buildsystem=meson dh_prep -O--buildsystem=meson dh_auto_install -O--buildsystem=meson cd obj-x86_64-linux-gnu && DESTDIR=/<>/blasr-5.3.3\+dfsg/debian/blasr LC_ALL=C.UTF-8 ninja install [1/4] Generating BlasrGitHash.h with a custom command [1/2] Installing files. Installing blasr to /<>/blasr-5.3.3+dfsg/debian/blasr/usr/bin Installing sawriter to /<>/blasr-5.3.3+dfsg/debian/blasr/usr/bin dh_install -O--buildsystem=meson dh_installdocs -O--buildsystem=meson dh_installchangelogs -O--buildsystem=meson dh_installman -O--buildsystem=meson dh_installinit -O--buildsystem=meson dh_installsystemduser -O--buildsystem=meson dh_lintian -O--buildsystem=meson dh_perl -O--buildsystem=meson dh_link -O--buildsystem=meson dh_strip_nondeterminism -O--buildsystem=meson dh_compress -O--buildsystem=meson dh_fixperms -O--buildsystem=meson dh_missing -O--buildsystem=meson dh_dwz -O--buildsystem=meson dh_strip -O--buildsystem=meson dh_makeshlibs -O--buildsystem=meson dh_shlibdeps -O--buildsystem=meson dh_installdeb -O--buildsystem=meson dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing blasr-dbgsym (in debian/.debhelper/blasr/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing blasr (in debian/blasr); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/blasr/DEBIAN/control, package blasr, directory debian/blasr pkgstripfiles: Truncating usr/share/doc/blasr/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package blasr ... pkgstripfiles: No PNG files. dpkg-deb: building package 'blasr' in '../blasr_5.3.3+dfsg-4build2_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/blasr/dbgsym-root/DEBIAN/control, package blasr-dbgsym, directory debian/.debhelper/blasr/dbgsym-root dpkg-deb: building package 'blasr-dbgsym' in 'debian/.debhelper/scratch-space/build-blasr/blasr-dbgsym_5.3.3+dfsg-4build2_amd64.deb'. Renaming blasr-dbgsym_5.3.3+dfsg-4build2_amd64.deb to blasr-dbgsym_5.3.3+dfsg-4build2_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../blasr_5.3.3+dfsg-4build2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200513-1749 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ blasr_5.3.3+dfsg-4build2_amd64.changes: --------------------------------------- Format: 1.8 Date: Wed, 13 May 2020 17:45:38 +0000 Source: blasr Binary: blasr Architecture: amd64 Version: 5.3.3+dfsg-4build2 Distribution: groovy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Graham Inggs Description: blasr - mapping single-molecule sequencing reads Changes: blasr (5.3.3+dfsg-4build2) groovy; urgency=medium . * No-change rebuild against libhdf5-103-1 Checksums-Sha1: 1725dde0755e8a199db9a82f199c01c3ddb0fd34 3517432 blasr-dbgsym_5.3.3+dfsg-4build2_amd64.ddeb 0afa1230c192034a8fec0a6ab0081d7aa12dda19 8327 blasr_5.3.3+dfsg-4build2_amd64.buildinfo 6dfd91927526589da17250df650bda5c24a9c471 226004 blasr_5.3.3+dfsg-4build2_amd64.deb Checksums-Sha256: 3d2ec7996167da9a8045c9dff7cac5d94829b83198f8ea0bc86d5910821f0451 3517432 blasr-dbgsym_5.3.3+dfsg-4build2_amd64.ddeb 3a90b1e035bbb29e781a433e76b19e3aee45b72c5bf3aa31600a31477846c2d8 8327 blasr_5.3.3+dfsg-4build2_amd64.buildinfo 55b4780159bb2fb073e772a868b5d92d99919b48824889c7926423bd3c335a50 226004 blasr_5.3.3+dfsg-4build2_amd64.deb Files: 9ee19ac7f0495cae256c274bde971c70 3517432 debug optional blasr-dbgsym_5.3.3+dfsg-4build2_amd64.ddeb 476a0a77b0b4bd33b60b8261af0302f5 8327 science optional blasr_5.3.3+dfsg-4build2_amd64.buildinfo 99090777fd05c84000f277e1860dda0f 226004 science optional blasr_5.3.3+dfsg-4build2_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ blasr_5.3.3+dfsg-4build2_amd64.deb ---------------------------------- new debian package, version 2.0. size 226004 bytes: control archive=1088 bytes. 866 bytes, 15 lines control 635 bytes, 10 lines md5sums Package: blasr Version: 5.3.3+dfsg-4build2 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 702 Depends: libblasr (>= 5.3.3+dfsg), libc6 (>= 2.29), libgcc-s1 (>= 3.0), libhdf5-cpp-103-1 (>= 1.10.5), libpbbam1.0.6 (>= 1.0.6+dfsg), libpbcopper1.3.0 (>= 1.6.0+dfsg), libstdc++6 (>= 9), libpbseq Section: science Priority: optional Homepage: https://github.com/PacificBiosciences/blasr Description: mapping single-molecule sequencing reads Basic local alignment with successive refinement (BLASR) is a method for mapping single-molecule sequencing reads against a reference genome. Such reads are thousands of bases long, with divergence between them and the genome being dominated by insertion and deletion error. drwxr-xr-x root/root 0 2020-05-13 17:45 ./ drwxr-xr-x root/root 0 2020-05-13 17:45 ./usr/ drwxr-xr-x root/root 0 2020-05-13 17:45 ./usr/bin/ -rwxr-xr-x root/root 633328 2020-05-13 17:45 ./usr/bin/blasr -rwxr-xr-x root/root 59872 2020-05-13 17:45 ./usr/bin/sawriter drwxr-xr-x root/root 0 2020-05-13 17:45 ./usr/share/ drwxr-xr-x root/root 0 2020-05-13 17:45 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-05-13 17:45 ./usr/share/doc/blasr/ -rw-r--r-- root/root 373 2020-01-22 16:48 ./usr/share/doc/blasr/NEWS.Debian.gz -rw-r--r-- root/root 1291 2019-03-11 18:23 ./usr/share/doc/blasr/README.md -rw-r--r-- root/root 41 2020-01-22 16:48 ./usr/share/doc/blasr/TODO.Debian -rw-r--r-- root/root 1276 2020-05-13 17:45 ./usr/share/doc/blasr/changelog.Debian.gz -rw-r--r-- root/root 2081 2020-01-22 16:48 ./usr/share/doc/blasr/copyright drwxr-xr-x root/root 0 2020-05-13 17:45 ./usr/share/lintian/ drwxr-xr-x root/root 0 2020-05-13 17:45 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 84 2020-01-22 16:48 ./usr/share/lintian/overrides/blasr drwxr-xr-x root/root 0 2020-05-13 17:45 ./usr/share/man/ drwxr-xr-x root/root 0 2020-05-13 17:45 ./usr/share/man/man1/ -rw-r--r-- root/root 1369 2020-05-13 17:45 ./usr/share/man/man1/blasr.1.gz -rw-r--r-- root/root 872 2020-05-13 17:45 ./usr/share/man/man1/sawriter.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 213972 Build-Time: 195 Distribution: groovy-proposed Host Architecture: amd64 Install-Time: 59 Job: blasr_5.3.3+dfsg-4build2.dsc Machine Architecture: amd64 Package: blasr Package-Time: 258 Source-Version: 5.3.3+dfsg-4build2 Space: 213972 Status: successful Version: 5.3.3+dfsg-4build2 -------------------------------------------------------------------------------- Finished at 20200513-1749 Build needed 00:04:18, 213972k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19299061 Scanning for processes to kill in build PACKAGEBUILD-19299061